<?xml version="1.0" encoding="UTF-8"?>
<!-- Copyright 2025 Filippo Rusconi <msxpertsuite@msxpertsuite.org> -->
<component type="desktop-application">
  <id>org.msxpertsuite.massxpert3</id>
  <metadata_license>CC-BY-SA-4.0</metadata_license>
  <project_license>GPL-3.0-or-later</project_license>
  <name>MsXpS mass spectrometry software</name>
  <summary>Model polymer chemistries and simulate mass spectrometric data</summary>

  <developer>Filippo Rusconi</developer>

  <icon type="stock">Massxpert3</icon>

  <description>

    <p>

      MassXpert (currently MassXpert3) is a program used to model polymer
      chemistries (like proteins or saccharides, for example) and use the
      models to simulate chemical reactions and mass spectral data obtained on
      the reaction products.

    </p>

    <p>The process can be summarized thusly:</p>

    <ul>

      <li>Define a brand new polymer chemistry (the package ships with complete
        definitions for proteins, nucleic acids and saccharides). Also, specify
        in any detail how the chemical entities should appear visually in the
        polymer sequence editor (monomer vignette, chemical modification vignette,
        cross-link vignette, for example; see the screenshots below).
      </li>

      <li>Edit a polymer sequence by first defining what polymer chemistry
        definition it is going to be;
      </li>

      <li>Start performing chemical simulations, like (bio-)chemical
        digestions, which produce oligomers (peptides for proteins, or
        oligosaccharides for saccharides, for example). This chemical action
        will generate the mass
        spectrometry data according to the mass calculation engine
        configuration (charge interval, partial cleavages...);
      </li>

      <li>Once the list of oligomers has been generated, select one of them and
        perform a gas-phase fragmentation. This new action also generates all
        the data that would be observed by performing the real fragmentation
        step in the mass spectrometer.
      </li>

      <li>If the isotopic cluster is of any interest (isotopic labelling
        experiments), select the formula of any chemical entity (oligomer
        [precursor ion], fragment [product ion] and compute the isotopic
        cluster for it.)
      </li>

      <li>The software contains a chemical calculator that is used like a
        desktop numerical calculator. The way the calculator works makes it
        possible to compute masses with atomic resolution. However, the
        calculator, which depends on the polymer chemistry definition, can cope
        with polymer sequences also.
      </li>

      <li>The software contains a JavaScript scripting interface that can be
        used to automate a number of tasks.
      </li>

    </ul>

  </description>

  <categories>
    <category>Science</category>
    <category>Education</category>
  </categories>

  <keywords>
    <keyword>Mass spectrometry</keyword>
    <keyword>Polymer chemistry</keyword>
    <keyword>Enzymatic digestion</keyword>
    <keyword>Chemical reaction</keyword>
    <keyword>Gas-phase fragmentation</keyword>
    <keyword>Product ion</keyword>
    <keyword>Precursor ion</keyword>
    <keyword>Chemical calculator</keyword>
    <keyword>Isotopic cluster</keyword>
    <keyword>Gaussian/Lorentzian shaper</keyword>
    <keyword>Mass spectrum</keyword>
  </keywords>

  <url type="homepage">http://www.msxpertsuite.org/massxpert/</url>
  <url type="help">http://www.msxpertsuite.org/massxpert/user-manual/</url>
  <url type="contact">http://www.msxpertsuite.org/contact/contact/</url>
  <url type="vcs-browser">https://codeberg.org/MsXpertSuite/MassXpert</url>

  <launchable type="desktop-id">org.msxpertsuite.MassXpert3.desktop</launchable>

  <releases>
    <release version="all">
      <description>This page lists all the releases. Check the tags also.</description>
      <url>https://codeberg.org/MsXpertSuite/MassXpert/releases</url>
      <issues>
        <issue url="https://codeberg.org/MsXpertSuite/MassXpert/issues"></issue>
      </issues>
    </release>
  </releases>

  <provides>
    <binary>MassXpert3</binary>
  </provides>

  <screenshots>

    <screenshot type="default">
      <caption>The main idea is that the user may define their polymer
        chemistry in as much detail as necessary
      </caption>
      <image>
        http://www.msxpertsuite.org/images/massxpert/xpertdef-overview.png
      </image>
    </screenshot>

    <screenshot>
      <caption>Once the polymer chemistry definition is complete, sequences of
        that definition might be edited
      </caption>
      <image>
        http://www.msxpertsuite.org/images/massxpert/xpertedit-overview.png
      </image>
    </screenshot>

    <screenshot>
      <caption>Typical applications of Massxpert are simulations of
        (bio-)chemical reactions and associated calculation of mass spectral
        data
      </caption>
      <image>
        http://www.msxpertsuite.org/images/massxpert/polymer-cleavage-mass-spectrum-simulation.png
      </image>
    </screenshot>

    <screenshot>
      <caption>Arbitrary mass search window</caption>
      <image>
        http://www.msxpertsuite.org/images/massxpert/arbitrary-mass-searches.png
      </image>
    </screenshot>

  </screenshots>

  <suggests>
    <id>org.msxpertsuite.minexpert3</id>
  </suggests>

  <update_contact>msxpertsuite@msxpersuite.org</update_contact>

  <references>
    <doi>10.1093/bioinformatics/btp504</doi>
    <registry name="MEDLINE">19740912</registry>
    <doi>doi: 10.1093/bioinformatics/18.4.644</doi>
    <registry name="MEDLINE">12016065</registry>
  </references>

</component>
